This is a wiki post. You can help me to create and better describe these issues or remove issues which don’t exist any longer. Please add screenshots where applicable.

The crash fix is now included in both Nightly and Bleeding Edge, so this workaround is not needed anymore. If you’re still crashing, please download the latest build.

Just because GitHub isn’t a support website, i’m moving the information from #2110 to the forums.

Backstory about this issue (for those who have no idea what this issue is):

The issue itself

Pokemon Super Mystery dungeon has a issue in Citra when identifying a 0x0 texture, which makes Citra crash. Currently, no work has been done, because we need a hardware test to see what the 3DS does in the same situation. But with the help of this forum thread, you could see a upcoming crash and disable the hardware renderer in time.

Crash locations:

After your personality test, you will see the opening credits. Next, you will see Deoxys flying toward the Earth. As the text is auto-scrolling, I would say disable it right as they try to speak. Keep it disabled until Rayquaza flies away from you.

Next, you will see some backgrounds of the landscape and then you start talking to yourself. When the player says “I can see something reflecting in the surface”, disable the renderer. Keep it disabled until the reflection on the water scene goes away.

Basically before every boss battle in the game. I don’t particulary have the last sentences from the bosses, but just try to disable it when some of the dialogue is passed. Keep it disabled until the white triangles go away.

Immediately after the Poliwrath Brothers boss battle. When you finish the boss battle, immediately turn the renderer off. Keep it disabled until you see Ampharos.

Second to hardest places to disable the renderer at the right time: The ghost scenes. Keep a progress device in case you crash and lose your progress.

5.1. Disable the renderer on the whole “Watchog on guard duty” scene.
5.2. Disable the renderer on the house scene with Farfetch’d and Audino.
5.3. Disable the renderer every time a Pokemon goes outside in the dark near the school. Also, this part also produces horrible sounds even at a low volume, so make sure to keep the sound as low as possible during those scenes to not get your ears blown away.
5.4. Disable the renderer after you arrive at the end of the Chapter 6 dungeon. Keep it disabled until the boss battle begins. Disable it again after defeating the boss.

The hardest place to disable the renderer at the right time: Fire Island Volcano. Keep a progress device in case you crash and lose your progress.

6.1. Disable the renderer before the few Pokemon battle. (The same rules as 3rd tip)
6.2. Disable the renderer before the boss legendary Pokemon. (The same rules as 3rd tip)
6.3. Disable the renderer when you lose intentionally and just before the legendary starts to come to you. Keep it disabled until yours and your partner scarves start to shine.
6.4. Disable the renderer before the rematch against the legendary Pokemon. (The same rules as 3rd tip)
6.5. This is the hardest part. If you want to continue after this point, you have to be very quick. Disable the renderer when the legendary Pokemon faints. The tricky part is seeing when that happens. You need to keep opening the Graphics menu just to be sure you don’t miss it. Keep it disabled until you get out of that dungeon.

In Chapter 16 you have a task to go after the bad guys. When you go up that dungeon, disable the renderer when you see the bad Pokemon. Keep it disabled until you get demolished and go to different dimension.

In Chapter 18, go through that dungeon and disable the renderer right after you climb to the top. Keep it disabled until you go back to the overworld.

The Tree of Life segment. Have a Progress Device in case you crash and lose your progress.
9.1. Go up the roots of the dungeon and disable right after you arrive at the trunk. Keep it disabled until the boss battle begins.
9.2. Disable the renderer right after you beat the boss. This one is much easier, because it gives us some free time to disable it. Keep it disabled until you can move again.
9.3. Final boss time! Disable the renderer just after you beat the first phase of the boss.
9.4. Disable the renderer after you beat the second stage of the boss. Keep it disabled until the cutscene goes away and you are brought next to the Tree of Life.

And you’re done! You beat the main game without any crashes! Congratulations!

Big thanks to knife-edge on GitHub, who found more places where the crashes happen.